ok, had a chance to check the pdf using acrobat 9 on mac 10.6.4. with overprint preview turned off, the green becomes almost white. however, once overprint preview is turned on, the green is quite visible and colour separates.
upon taking the pdf into illustrator to work out WTF is going on, i discovered that (when the overprint preview was off) the green becomes almost white, but again with the overprint on, the green goes green. however, while in illustrator, i placed the cursor on the solid green fill at the bottom and found a white fill which was set to overprint. once that was deleted, the green beneath was visible. I think this is the problem which your printer is talking about, because many RIPs have an action which forces any white to knockout, which is a normal thing to do, but once that happens, then the preview becomes almost white.
I think this problem is actually created by this paragraph in the indesignsecrets.com article:
Now you need to make sure your pages are going to get flattened. For each spread that contains text that you want converted to outlines, put a transparency object on it. If you want to convert every page, you can put this object on your master pages. For example, it could be an object with a Tint of .1% and an Opacity of .01% off on the margin that will never be seen. Or you could make a one-pixel large Photoshop file with a transparent background and place it on your pages.
after looking at the pdf, it looks like a white box was drawn over the entire artwork and then set to the tint/opacity as mentioned above BUT sent to the front. the advice above suggests that this only has to be done in a margin, not within the page and certainly not encompassing the entire artwork. the paragraph is unclear though and an illustration explaining this within the tip would have helped.
i'm not sure why the OP is going to such lengths to try and convert all text to paths and IMHO its completely unnecessary if the PDF is made using PDF standard PDF/X-1a (or PDF/X-3 for remaining transparency) as mentioned by Eelco in this post. i've read the original tip and many posts placed after the tip and feel that, unless files are being sent to older RIPs (like, WAY older) or the pdfs are being dealt with unusually (e.g. opened up in corel draw and then printed to a plotter – i've heard of this happening!) then PDFs should be fine. simply, if the PDF being supplied is to pass through a level 3 RIP, then outlining fonts is unnecessary if the pdf is made properly.
my buck o'five